  anonymous_namespace{abstractoptionstorage.cpp} | |
   MockOptionStorage | Mock implementation of an option storage class for unit testing |
 MockOption | Specifies an option that has a mock storage object for unit testing |
| anonymous_namespace{analysisdata.cpp} | |
| anonymous_namespace{angle.cpp} | |
| anonymous_namespace{arraydata.cpp} | |
| anonymous_namespace{average.cpp} | |
| anonymous_namespace{basicoptions.cpp} | |
| anonymous_namespace{binaryinformation.cpp} | |
| anonymous_namespace{cmdlinehelpmodule.cpp} | |
| anonymous_namespace{cmdlinehelpwriter.cpp} | |
| anonymous_namespace{cmdlinemodulemanager.cpp} | |
| anonymous_namespace{cmdlineparser.cpp} | |
| anonymous_namespace{cmdlineprogramcontext.cpp} | |
| anonymous_namespace{cmdlinerunner.cpp} | |
| anonymous_namespace{compressed_x_output.cpp} | |
| MdrunCompressedXOutputTest | Test fixture for mdrun -x |
| anonymous_namespace{confio.cpp} | |
| anonymous_namespace{cpuinfo.cpp} | |
| anonymous_namespace{distance.cpp} | |
| anonymous_namespace{domain_decomposition.cpp} | |
| DomainDecompositionSpecialCasesTest | Test fixture for domain decomposition special cases |
| anonymous_namespace{electricfield.cpp} | |
| anonymous_namespace{evaluate.cpp} | |
| MempoolSelelemReserver | Reserves memory for a selection element from the evaluation memory pool |
| MempoolGroupReserver | Reserves memory for an index group from the evaluation memory pool |
| SelelemTemporaryValueAssigner | Assigns a temporary value for a selection element |
| anonymous_namespace{fft.cpp} | |
| anonymous_namespace{filenameoption.cpp} | |
| anonymous_namespace{filenameoptionmanager.cpp} | |
| anonymous_namespace{freevolume.cpp} | |
| anonymous_namespace{functions.cpp} | |
| anonymous_namespace{genconf.cpp} | |
| anonymous_namespace{gmx_awh.cpp} | |
| anonymous_namespace{gmx_traj.cpp} | |
| anonymous_namespace{gmx_trjconv.cpp} | |
| anonymous_namespace{grompp.cpp} | |
| GromppTest | Test fixture for grompp |
| anonymous_namespace{hardwaretopology.cpp} | |
| anonymous_namespace{helpformat.cpp} | |
| anonymous_namespace{helpmanager.cpp} | |
| anonymous_namespace{helpwritercontext.cpp} | |
| anonymous_namespace{histogram.cpp} | |
| MockAverageHistogram | Mock object for testing gmx::AbstractAverageHistogram |
| anonymous_namespace{indexutil.cpp} | |
| anonymous_namespace{insert-molecules.cpp} | |
| anonymous_namespace{interactivetest.cpp} | |
| anonymous_namespace{invertmatrix.cpp} | |
| anonymous_namespace{keyvaluetreeserializer.cpp} | |
| anonymous_namespace{keyvaluetreetransform.cpp} | |
| anonymous_namespace{legacymodules.cpp} | Registers command-line modules for pre-5.0 binaries |
| ObsoleteToolModule | Command line module that provides information about obsolescence |
| anonymous_namespace{lifetime.cpp} | |
| anonymous_namespace{listed-forces.cpp} | |
| anonymous_namespace{logger.cpp} | |
| anonymous_namespace{mdrun_main.cpp} | |
| anonymous_namespace{mpitest.cpp} | |
| anonymous_namespace{nbsearch.cpp} | |
| anonymous_namespace{option.cpp} | |
| anonymous_namespace{optionsassigner.cpp} | |
| anonymous_namespace{pairdist.cpp} | |
| anonymous_namespace{pargs.cpp} | |
| anonymous_namespace{parsetree.cpp} | |
| anonymous_namespace{path.cpp} | |
| anonymous_namespace{plot.cpp} | |
| anonymous_namespace{poscalc.cpp} | |
| anonymous_namespace{position-restraints.cpp} | |
| anonymous_namespace{rdf.cpp} | |
| anonymous_namespace{readir.cpp} | |
| anonymous_namespace{refdata_tests.cpp} | |
| anonymous_namespace{repeatingsection.cpp} | |
| anonymous_namespace{rerun.cpp} | |
| MdrunRerun | Test fixture for mdrun -rerun |
| anonymous_namespace{resourcedivision.cpp} | |
| SingleRankChecker | Handles checks for algorithms that must use a single rank |
| anonymous_namespace{sasa.cpp} | |
| anonymous_namespace{select.cpp} | |
| anonymous_namespace{selectioncollection.cpp} | |
| anonymous_namespace{selectionoption.cpp} | |
| anonymous_namespace{selhelp.cpp} | |
| anonymous_namespace{shake.cpp} | |
| ShakeTest | Test fixture for testing SHAKE |
| anonymous_namespace{sm_keywords.cpp} | |
| StringKeywordMatchItem | Single item in the list of strings/regular expressions to match |
| t_methoddata_kwstr | Data structure for string keyword expression evaluation |
| anonymous_namespace{solvate.cpp} | |
| anonymous_namespace{surfacearea.cpp} | |
| anonymous_namespace{sysinfo.cpp} | |
| anonymous_namespace{testasserts_tests.cpp} | |
| anonymous_namespace{textwriter.cpp} | |
| anonymous_namespace{threadaffinity-mpi.cpp} | |
| anonymous_namespace{threadaffinity.cpp} | |
| anonymous_namespace{timeunitmanager.cpp} | |
| anonymous_namespace{tngio.cpp} | |
| anonymous_namespace{trajectory.cpp} | |
| anonymous_namespace{trajectory_writing.cpp} | |
| anonymous_namespace{treesupport.cpp} | |
| anonymous_namespace{unionfind.cpp} | |
| anonymous_namespace{vectypes.cpp} | |
| anonymous_namespace{xvgtest_tests.cpp} | |
| gmx | Generic GROMACS namespace |
| analysismodules | |
| anonymous_namespace{angle.cpp} | |
| AnglePositionIterator | Helper to encapsulate logic for looping over input selections |
| anonymous_namespace{distance.cpp} | |
| anonymous_namespace{freevolume.cpp} | |
| FreeVolume | Class used to compute free volume in a simulations box |
| anonymous_namespace{pairdist.cpp} | |
| PairDistance | Implements gmx pairdist trajectory analysis module |
| PairDistanceModuleData | Temporary memory for use within a single-frame calculation |
| anonymous_namespace{rdf.cpp} | |
| Rdf | Implements gmx rdf trajectory analysis module |
| RdfModuleData | Temporary memory for use within a single-frame calculation |
| anonymous_namespace{sasa.cpp} | |
| t_conect | Tracks information on two nearest neighbors of a single surface dot |
| Sasa | Implements gmx sas trajectory analysis module |
| SasaModuleData | Temporary memory for use within a single-frame calculation |
| anonymous_namespace{select.cpp} | |
| IndexFileWriterModule | Data module for writing index files |
| anonymous_namespace{trajectory.cpp} | |
| anonymous_namespace{alignedallocator.cpp} | |
| anonymous_namespace{analysismodule.cpp} | |
| TrajectoryAnalysisModuleDataBasic | Basic thread-local trajectory analysis data storage class |
| anonymous_namespace{arrayref.cpp} | |
| anonymous_namespace{autocorr.cpp} | |
| anonymous_namespace{biasparams.cpp} | |
| anonymous_namespace{biasstate.cpp} | |
| anonymous_namespace{biaswriter.cpp} | |
| anonymous_namespace{bonded.cpp} | |
| anonymous_namespace{boxutilities.cpp} | |
| anonymous_namespace{calc_verletbuf.cpp} | |
| anonymous_namespace{cmdlinehelpcontext.cpp} | |
| anonymous_namespace{cmdlinehelpmodule.cpp} | |
| RootHelpTopic | Help topic that forms the root of the help tree for the help subcommand |
| IHelpExport | Callbacks for exporting help information for command-line modules |
| CommandsHelpTopic | Help topic for listing the commands |
| ModuleHelpTopic | Help topic wrapper for a command-line module |
| HelpExportReStructuredText | Implements export for web pages as reStructuredText |
| HelpExportCompletion | Implements export for command-line completion |
| anonymous_namespace{cmdlinehelpwriter.cpp} | |
| IOptionsFormatter | Interface for output format specific formatting of options |
| OptionsFilter | Output format independent processing of options |
| SynopsisFormatter | Formatter implementation for synopsis |
| OptionsListFormatter | Formatter implementation for help export |
| anonymous_namespace{cmdlineinit.cpp} | |
| anonymous_namespace{cmdlinemodulemanager.cpp} | |
| CMainCommandLineModule | Implements a ICommandLineModule, given a function with C/C++ main() signature |
| anonymous_namespace{cmdlineoptionsmodule.cpp} | |
| anonymous_namespace{cmdlineprogramcontext.cpp} | |
| DefaultExecutableEnvironment | Default implementation for IExecutableEnvironment |
| anonymous_namespace{cmdlinerunner.cpp} | |
| anonymous_namespace{coolstuff.cpp} | |
| anonymous_namespace{coordstate.cpp} | |
| anonymous_namespace{correlationgrid.cpp} | |
| anonymous_namespace{correlationtensor.cpp} | |
| anonymous_namespace{cpuinfo.cpp} | |
| ApicIdLayout | The layout of the bits in the APIC ID |
| anonymous_namespace{cubicsplinetable.cpp} | |
| anonymous_namespace{decidegpuusage.cpp} | |
| anonymous_namespace{devicetransfers_ocl.cpp} | |
| anonymous_namespace{electricfield.cpp} | |
| ElectricFieldData | Declaration of storage unit for fields |
| ElectricField | Describe time dependent electric field |
| anonymous_namespace{errorcodes.cpp} | |
| anonymous_namespace{exceptions.cpp} | |
| ErrorMessage | Error message or error context text item |
| IMessageWriter | Abstracts actual output from the other logic in exception formatting |
| MessageWriterFileNoThrow | Exception information writer for cases where exceptions should be avoided |
| MessageWriterTextWriter | Exception information writer to format into a TextOutputStream |
| MessageWriterString | Exception information writer to format into an std::string |
| anonymous_namespace{expfit.cpp} | |
| anonymous_namespace{exponentialdistribution.cpp} | |
| anonymous_namespace{filenameoption.cpp} | |
| FileTypeMapping | Mapping from OptionFileType to a file type in filetypes.h |
| FileTypeHandler | Handles a single file type known to FileNameOptionStorage |
| anonymous_namespace{filenameoptionmanager.cpp} | |
| anonymous_namespace{fileredirector.cpp} | |
| DefaultInputRedirector | Implements the redirector returned by defaultFileInputRedirector() |
| DefaultOutputRedirector | Implements the redirector returned by defaultFileOutputRedirector() |
| anonymous_namespace{filestream.cpp} | |
| anonymous_namespace{findallgputasks.cpp} | |
| anonymous_namespace{futil.cpp} | |
| anonymous_namespace{gammadistribution.cpp} | |
| anonymous_namespace{grid.cpp} | |
| anonymous_namespace{hardwaretopology.cpp} | |
| anonymous_namespace{helpwritercontext.cpp} | |
| IWrapper | Custom output interface for HelpWriterContext::Impl::processMarkup() |
| WrapperToString | Wraps markup output into a single string |
| WrapperToVector | Wraps markup output into a vector of string (one line per element) |
| anonymous_namespace{histogram.cpp} | |
| StaticAverageHistogram | Represents copies of average histograms |
| anonymous_namespace{histogramsize.cpp} | |
| anonymous_namespace{hostallocator.cpp} | |
| HostMemoryTest | Typed test fixture for infrastructure for host-side memory used for GPU transfers |
| HostAllocatorTest | Typed test fixture |
| anonymous_namespace{identifyavx512fmaunits.cpp} | |
| anonymous_namespace{ikeyvaluetreeerror.cpp} | |
| anonymous_namespace{init.cpp} | |
| anonymous_namespace{inmemoryserializer.cpp} | |
| anonymous_namespace{insert-molecules.cpp} | |
| anonymous_namespace{keyvaluetree.cpp} | |
| anonymous_namespace{keyvaluetreeserializer.cpp} | |
| anonymous_namespace{keyvaluetreetransform.cpp} | |
| anonymous_namespace{logger.cpp} | |
| anonymous_namespace{make_unique.cpp} | |
| anonymous_namespace{manyautocorrelation.cpp} | |
| anonymous_namespace{modules.cpp} | |
| anonymous_namespace{nbsearch.cpp} | |
| MindistAction | Search action find the minimum distance |
| anonymous_namespace{normaldistribution.cpp} | |
| anonymous_namespace{optionsection.cpp} | |
| anonymous_namespace{optionsvisitor.cpp} | |
| anonymous_namespace{pargs.cpp} | |
| OptionsAdapter | Conversion helper between t_pargs/t_filenm and Options |
| anonymous_namespace{pointstate.cpp} | |
| anonymous_namespace{pointstate.h} | |
| anonymous_namespace{poscalc.cpp} | |
| anonymous_namespace{programcontext.cpp} | |
| DefaultProgramContext | Default implementation of IProgramContext |
| anonymous_namespace{pull.cpp} | |
| anonymous_namespace{quadraticsplinetable.cpp} | |
| anonymous_namespace{reportgpuusage.cpp} | |
| anonymous_namespace{rstparser.cpp} | |
| anonymous_namespace{seed.cpp} | |
| anonymous_namespace{selectioncollection.cpp} | |
| anonymous_namespace{selhelp.cpp} | |
| KeywordDetailsHelpTopic | Help topic implementation for an individual selection method |
| KeywordsHelpTopic | Custom help topic for printing a list of selection keywords |
| anonymous_namespace{shellcompletions.cpp} | |
| anonymous_namespace{simd_memory.cpp} | |
| anonymous_namespace{stringutil.cpp} | |
| anonymous_namespace{tabulatednormaldistribution.cpp} | |
| anonymous_namespace{tabulatednormaldistribution.h} | |
| anonymous_namespace{taskassignment.cpp} | |
| anonymous_namespace{threefry.cpp} | |
| anonymous_namespace{timeunitmanager.cpp} | |
| TimeOptionScaler | Option visitor that scales time options |
| anonymous_namespace{treesupport.cpp} | |
| anonymous_namespace{uniformintdistribution.cpp} | |
| anonymous_namespace{uniformrealdistribution.cpp} | |
| compat | Compatibility aliases for standard library features |
| internal | Internal GROMACS namespace |
| anonymous_namespace{selection.cpp} | |
| AnalysisDataHandleImpl | Private implementation class for AnalysisDataHandle |
| AnalysisDataStorageImpl | Private implementation class for AnalysisDataStorage |
| AnalysisDataStorageFrameData | Internal representation for a single stored frame |
| BasicAverageHistogramModule | Implements average histogram module that averages per-frame histograms |
| BasicHistogramImpl | Base class for private implementation classes for histogram modules |
| EnumIndexStore | Type-specific implementation for IOptionValueStore for an enum option |
| OptionSectionImpl | Internal implementation class for storing an option section |
| Group | Describes a group of options (see Options::addGroup()) |
| OptionsImpl | Private implementation class for Options |
| SelectionData | Internal data for a single selection |
| SimdTraits | Simd traits |
| SimdArrayRef | STL-like container for aligned SIMD type. Used as ArrayRef<SimdReal> |
| IExceptionInfo | Base class for ExceptionInfo |
| test | Testing utilities namespace |
| anonymous_namespace{base.cpp} | |
| anonymous_namespace{bootstrap_loadstore.cpp} | |
| anonymous_namespace{clustsize.cpp} | |
| anonymous_namespace{cmdlinemodulemanagertest.cpp} | |
| anonymous_namespace{conftest.cpp} | |
| anonymous_namespace{filematchers.cpp} | |
| anonymous_namespace{initialconstraints.cpp} | |
| InitialConstraintsTest | Test fixture parametrized on integrators |
| anonymous_namespace{legacyenergy.cpp} | |
| anonymous_namespace{loggertest.cpp} | |
| anonymous_namespace{mdebin.cpp} | |
| anonymous_namespace{mdruncomparisonfixture.cpp} | |
| anonymous_namespace{mock_datamodule.cpp} | |
| StaticDataFrameHeaderChecker | Functor for checking data frame header against static test input data |
| StaticDataPointsChecker | Functor for checking data frame points against static test input data |
| DataStorageRequester | Functor for requesting data storage |
| StaticDataPointsStorageChecker | Functor for checking data frame points and storage against static test input data |
| anonymous_namespace{moduletest.cpp} | |
| anonymous_namespace{mutex.cpp} | |
| DifferentTasksTest | Parameterized test fixture |
| anonymous_namespace{pinnedmemorychecker.cpp} | |
| anonymous_namespace{pmebsplinetest.cpp} | |
| PmeBSplineModuliTest | Test fixture for testing PME B-spline moduli creation |
| anonymous_namespace{pmegathertest.cpp} | |
| AtomAndPmeOrderSizedData | A structure for all the spline data which depends in size both on the PME order and atom count |
| AtomSizedData | A structure for all the input atom data which depends in size on atom count - including a range of spline data for different PME orders |
| PmeGatherTest | Test fixture |
| anonymous_namespace{pmesolvetest.cpp} | |
| PmeSolveTest | Test fixture |
| anonymous_namespace{pmesplinespreadtest.cpp} | |
| PmeSplineAndSpreadTest | Test fixture for testing both atom spline parameter computation and charge spreading. These 2 stages of PME are tightly coupled in the code |
| anonymous_namespace{pmetest.cpp} | |
| PmeTest | A basic PME runner |
| anonymous_namespace{refdata-xml.cpp} | |
| anonymous_namespace{refdata.cpp} | |
| anonymous_namespace{scalar.cpp} | |
| anonymous_namespace{scalar_math.cpp} | |
| anonymous_namespace{scalar_util.cpp} | |
| anonymous_namespace{simd4_floatingpoint.cpp} | |
| anonymous_namespace{simd4_math.cpp} | |
| anonymous_namespace{simd4_vector_operations.cpp} | |
| anonymous_namespace{simd_floatingpoint.cpp} | |
| anonymous_namespace{simd_floatingpoint_util.cpp} | |
| SimdFloatingpointUtilTest | Test fixture for higher-level floating-point utility functions |
| anonymous_namespace{simd_integer.cpp} | |
| anonymous_namespace{simd_math.cpp} | |
| anonymous_namespace{simd_vector_operations.cpp} | |
| anonymous_namespace{splinetable.cpp} | |
| SplineTableTest | Test fixture for table comparision with analytical/numerical functions |
| anonymous_namespace{stringtest.cpp} | |
| anonymous_namespace{stringutil.cpp} | |
| anonymous_namespace{testasserts.cpp} | |
| anonymous_namespace{testasserts.h} | |
| anonymous_namespace{testinit.cpp} | |
| TestProgramContext | Custom program context for test binaries |
| anonymous_namespace{testoptions.cpp} | |
| TestOptionsRegistry | Singleton registry for test options added with GMX_TEST_OPTIONS |
| anonymous_namespace{textblockmatchers.cpp} | |
| anonymous_namespace{textreader.cpp} | |
| TextReaderTestParams | Helper struct |
| TextReaderTest | Test fixture |
| anonymous_namespace{usergpuids.cpp} | |
| anonymous_namespace{xvgtest.cpp} | |
| internal | |
| TestReferenceDataImpl | Private implementation class for TestReferenceData |
| AnalysisDataTestInputPointSet | Represents a single set of points in AnalysisDataTestInputFrame structure |
| AnalysisDataTestInputFrame | Represents a single frame in AnalysisDataTestInput structure |
| AnalysisDataTestInput | Represents static input data for AbstractAnalysisData tests |
| AnalysisDataTestFixture | Test fixture for AbstractAnalysisData testing |
| AwhTestParameters | Struct that gathers all input for setting up and using a Bias |
| BiasTest | Test fixture for testing Bias updates |
| BiasStateTest | Test fixture for testing Bias updates |
| MockModule | Mock implementation of gmx::ICommandLineModule |
| MockOptionsModule | Mock implementation of gmx::ICommandLineOptionsModule |
| CommandLineModuleManagerTestBase | Test fixture for tests using gmx::CommandLineModuleManager |
| TestHardwareContext | A structure to describe a hardware context - an abstraction over gmx_device_info_t with a human-readable string. TODO: currently this does not know which CodePath it belongs too. It probably should! That would save us one loop in all the PME tests |
| PmeTestEnvironment | This class performs one-time test initialization (enumerating the hardware) |
| SettleTest | Test fixture for testing SETTLE position updates |
| SignalTest | Test fixture for mdrun signalling |
| SimdBaseTest | Base class for SIMD test fixtures |
| SimdTest | Test fixture for SIMD tests |
| Simd4Test | Test fixture for SIMD4 tests - contains test settings |
| AbstractTrajectoryAnalysisModuleTestFixture | Test fixture for trajectory analysis modules |
| TrajectoryAnalysisModuleTestFixture | Test fixture for a trajectory analysis module |
| AllocatorTest | Templated test fixture |
| EnergyFrameReader | Manages returning an EnergyFrame containing required energy field values read from successive frames of an .edr file |
| EnergyFrame | Contains the content of an .edr frame read by an EnergyFrameReader |
| MdrunComparisonFixture | Declares abstract base text fixture class for integration tests of mdrun functionality that will compare multiple calls to mdrun |
| SimulationRunner | Helper object for running grompp and mdrun in integration tests of mdrun functionality |
| MdrunTestFixtureBase | Declares test fixture base class for integration tests of mdrun functionality |
| MdrunTestFixture | Declares test fixture class for integration tests of mdrun functionality that use a single call of mdrun |
| ParameterizedMdrunTestFixture | Parameterized test fixture for mdrun integration tests |
| MultiSimTest | Test fixture for multi-sim functionality |
| BondedInteractionsTest | Test fixture for bonded interactions |
| TerminationHelper | Help test mdrun termination behaviour |
| TrajectoryFrameReader | Manages returning a t_trxframe whose contents were read from successive frames of an trajectory file |
| TrajectoryFrame | Contains the content of a trajectory frame read by an TrajectoryFrameReader |
| CommandLine | Helper class for tests that need to construct command lines |
| CommandLineTestHelper | Helper class for tests that construct command lines that need to reference existing files |
| CommandLineTestBase | Test fixture for tests that call a single command-line program with input/output files |
| ConfMatch | Match the contents as an gro file |
| IFileMatcher | Represents a file matcher, matching file contents against reference (or other) data |
| IFileMatcherSettings | Represents a factory for creating a file matcher |
| TextFileMatch | Use a ITextStreamMatcher for matching the contents |
| NoContentsMatch | Do not check the contents of the file |
| InteractiveTestHelper | Helper class for testing interactive sessions |
| LoggerTestHelper | Helper class for tests to check output written to a logger |
| TestReferenceChecker | Handles comparison to test reference data |
| Impl | Private implementation class for TestReferenceChecker |
| TestReferenceData | Handles creation of and comparison to test reference data |
| StdioTestHelper | Helper class for tests where code reads directly from stdin |
| StringTestBase | Test fixture for tests that check string formatting |
| FloatingPointDifference | Computes and represents a floating-point difference value |
| FloatingPointTolerance | Specifies a floating-point comparison tolerance and checks whether a difference is within the tolerance |
| TestException | Exception class for reporting errors in tests |
| TestFileManager | Helper for tests that need input and output files |
| Impl | Private implementation class for TestFileManager |
| TestFileInputRedirector | In-memory implementation for IFileInputRedirector for tests |
| TestFileOutputRedirector | In-memory implementation of IFileOutputRedirector for tests |
| TestOptionsProvider | Provides additional options for the test executable |
| ITextBlockMatcher | Represents a text matcher, matching text stream contents against reference data |
| ITextBlockMatcherSettings | Represents a factory for creating a text matcher |
| ExactTextMatch | Use an exact text match (the contents should be exactly equal) |
| NoTextMatch | Do not match the text (the contents are ignored) |
| XvgMatch | Match the contents as an xvg file |
| AbstractAnalysisData | Abstract base class for all objects that provide data |
| Impl | Private implementation class for AbstractAnalysisData |
| AnalysisData | Parallelizable data container for raw data |
| Impl | Private implementation class for AnalysisData |
| AnalysisDataHandle | Handle for inserting data into AnalysisData |
| AbstractAnalysisArrayData | Abstract base class for data objects that present in-memory data |
| AnalysisArrayData | Simple in-memory data array |
| AnalysisDataValue | Value type for representing a single value in analysis data objects |
| AnalysisDataFrameHeader | Value type for storing frame-level information for analysis data |
| AnalysisDataPointSetRef | Value type wrapper for non-mutable access to a set of data column values |
| AnalysisDataFrameRef | Value type wrapper for non-mutable access to a data frame |
| IAnalysisDataModule | Interface for a module that gets notified whenever data is added |
| AnalysisDataModuleSerial | Convenience base class for serial analysis data modules |
| AnalysisDataModuleParallel | Convenience base class for parallel analysis data modules |
| AnalysisDataModuleManager | Encapsulates handling of data modules attached to AbstractAnalysisData |
 Impl | Private implementation class for AnalysisDataModuleManager |
 ModuleInfo | Stores information about an attached module |
| AnalysisDataProxy | Internal implementation class used to implement column modules |
| AnalysisDataStorageFrame | Allows assigning values for a data frame in AnalysisDataStorage |
| AnalysisDataStorage | Helper class that implements storage of data |
| AnalysisDataFrameLocalDataSetHandle | Handle to a single data set within frame-local data array |
| AnalysisDataFrameLocalDataHandle | Handle to a single frame data within frame-local data array |
| AnalysisDataFrameLocalData | Container for an array of frame-local values that supports parallel data processing |
| AnalysisDataAverageModule | Data module for independently averaging each column in input data |
| AnalysisDataFrameAverageModule | Data module for averaging of columns for each frame |
| AnalysisDataDisplacementModule | Data module for calculating displacements |
| Impl | Private implementation class for AnalysisDataDisplacementModule |
| AnalysisDataFrameAverager | Helper class for modules that average values over frames |
| AnalysisHistogramSettingsInitializer | Provides "named parameter" idiom for constructing histograms |
| AnalysisHistogramSettings | Contains parameters that specify histogram bin locations |
| AbstractAverageHistogram | Base class for representing histograms averaged over frames |
| AnalysisDataSimpleHistogramModule | Data module for per-frame histograms |
| Impl | Private implementation class for AnalysisDataSimpleHistogramModule |
| AnalysisDataWeightedHistogramModule | Data module for per-frame weighted histograms |
| Impl | Private implementation class for AnalysisDataWeightedHistogramModule |
| AnalysisDataBinAverageModule | Data module for bin averages |
| AnalysisDataLifetimeModule | Data module for computing lifetime histograms for columns in input data |
| Impl | Private implementation class for AnalysisDataLifetimeModule |
| AnalysisDataPlotSettings | Common settings for data plots |
| AbstractPlotModule | Abstract data module for writing data into a file |
| AnalysisDataPlotModule | Plotting module for straightforward plotting of data |
| AnalysisDataVectorPlotModule | Plotting module specifically for data consisting of vectors |
| AnalysisDataParallelOptions | Parallelization options for analysis data objects |
| BiasCoupledToSystem | A bias and its coupling to the system |
| Awh | Coupling of the accelerated weight histogram method (AWH) with the system |
| Bias | A bias acting on a multidimensional coordinate |
| BiasParams | Constant parameters for the bias |
| BiasState | The state of a bias |
| AwhEnergyBlock | AWH output data block that can be written to an energy file block |
| BiasWriter | Class organizing the output data storing and writing of an AWH bias |
| CoordState | Keeps track of the current coordinate value, grid index and umbrella location |
| CorrelationGrid | Grid of local correlation tensors |
| CorrelationBlockData | Correlation block averaging weight-only data |
| CoordData | Correlation block averaging data |
| CorrelationTensor | Correlation data for computing the correlation tensor of one grid point |
| DimParams | Constant parameters for each dimension of the coordinate |
| GridAxis | An axis, i.e. dimension, of the grid |
| GridPoint | A point in the grid |
| Grid | The grid, generally multidimensional and periodic |
| HistogramSize | Tracks global size related properties of the bias histogram |
| PointState | The state of a coordinate point |
| CommandLineHelpContext | Context information for writing out command-line help |
| Impl | Private implementation class for CommandLineHelpContext |
| GlobalCommandLineHelpContext | Helper for passing CommandLineHelpContext into parse_common_args() |
| CommandLineHelpModule | Command-line module for producing help |
| ArrayRef | STL-like container for an interface to a C array of T (or part of a std::vector<T, A> or std::array<T>) |
| CommandLineHelpWriter | Writes help information for Options |
| Impl | Private implementation class for CommandLineHelpWriter |
| CommandLineModuleSettings | Settings to pass information between a module and the general runner |
| ICommandLineModule | Module that can be run from command line using CommandLineModuleManager |
| CommandLineModuleGroupData | Internal data for a CommandLineModuleManager module group |
| CommandLineCommonOptionsHolder | Encapsulates some handling of common options to the wrapper binary |
| CommandLineModuleManager | Implements a wrapper command-line interface for multiple modules |
| Impl | Private implementation class for CommandLineModuleManager |
| CommandLineModuleGroup | Handle to add content to a group added with CommandLineModuleManager::addModuleGroup() |
| ICommandLineOptionsModuleSettings | Settings to pass information between a CommandLineOptionsModule and generic code that runs it |
| ICommandLineOptionsModule | Module that can be run from a command line and uses gmx::Options for argument processing |
| CommandLineParser | Implements command-line parsing for Options objects |
| Impl | Private implementation class for CommandLineParser |
| IExecutableEnvironment | Allows customization of the way various directories are found by CommandLineProgramContext |
| CommandLineProgramContext | Program context implementation for command line programs |
| HostAllocationPolicy | Policy class for configuring gmx::Allocator, to manage allocations of memory that may be needed for e.g. GPU transfers |
| Impl | Private implementation class |
| CpuInfo | Detect CPU capabilities and basic logical processor info |
| LogicalProcessor | Entry with basic information for a single logical processor |
| HardwareTopology | Information about sockets, cores, threads, numa, caches |
| Cache | Information about a single cache level |
| Core | Information about a single core in a socket |
| Device | Information about a single PCI device |
| HWThread | Information about a single hardware thread in a core |
| LogicalProcessor | Information about socket, core and hwthread for a logical processor |
| Machine | Hardware topology information about the entire machine |
| Numa | Information about a single numa node |
| NumaNode | Information about each numa node in system |
| Socket | Information about a single socket in the system |
| StaticLog2 | Evaluate log2(n) for integer n statically at compile time |
| StaticLog2< 1 > | Specialization of StaticLog2<n> for n==1 |
| StaticLog2< 0 > | Specialization of StaticLog2<n> for n==0 |
| BasicVector | C++ class for 3D vectors |
| MDAtoms | Contains a C-style t_mdatoms while managing some of its memory with C++ vectors with allocators |
| SimulationSignal | POD-style object used by mdrun ranks to set and receive signals within and between simulations |
| SimulationSignaller | Object used by mdrun ranks to signal to each other at this step |
| MDModules | Manages the collection of all modules used for mdrun |
| ForceWithVirial | Container for force and virial for algorithms that provide their own virial tensor contribution |
| IForceProvider | Interface for a component that provides forces during MD |
| IMDModule | Extension module for GROMACS simulations |
| IMDOutputProvider | Interface for handling additional output files during a simulation |
| IMdpOptionProvider | Interface for handling mdp/tpr input to a mdrun module |
| TextTableFormatter | Formats rows of a table for text output |
| Impl | Private implementation class for TextTableFormatter |
| ColumnData | Manages a single column for TextTableFormatter |
| HelpManager | Helper for providing interactive online help |
| Impl | Private implementation class for HelpManager |
| AbstractSimpleHelpTopic | Abstract base class for help topics that have simple text and no subtopics |
| AbstractCompositeHelpTopic | Abstract base class for help topics that have simple text and subtopics |
| Impl | Private implementation class for AbstractCompositeHelpTopic |
| SimpleHelpTopic | Template for simple implementation of AbstractSimpleHelpTopic |
| CompositeHelpTopic | Template for simple implementation of AbstractCompositeHelpTopic |
| HelpLinks | Hyperlink data for writing out help |
| Impl | Private implementation class for HelpLinks |
| HelpWriterContext | Context information for writing out help |
| Impl | Private implementation class for HelpWriterContext |
| SharedState | Shared, non-modifiable state for context objects |
| IHelpTopic | Provides a single online help topic |
| RstParagraphIterator | Iterator over reStructuredText paragraphs |
| OptionStorageTemplate | Templated base class for constructing option value storage classes |
| AbstractOption | Abstract base class for specifying option properties |
| OptionTemplate | Templated base class for constructing concrete option settings classes |
| OptionInfo | Gives information and allows modifications to an option after creation |
| AbstractOptionStorage | Abstract base class for converting, validating, and storing option values |
| AbstractOptionSection | Base class for specifying option section properties |
| AbstractOptionSectionHandle | Base class for handles to option sections |
| BooleanOption | Specifies an option that provides boolean values |
| IntegerOption | Specifies an option that provides integer values |
| Int64Option | Specifies an option that provides 64-bit integer values |
| DoubleOption | Specifies an option that provides floating-point (double) values |
| FloatOption | Specifies an option that provides floating-point (float) values |
| StringOption | Specifies an option that provides string values |
| EnumOption | Specifies an option that accepts enumerated string values and writes the selected index into an enum variable |
| BooleanOptionInfo | Wrapper class for accessing boolean option information |
| IntegerOptionInfo | Wrapper class for accessing integer option information |
| Int64OptionInfo | Wrapper class for accessing 64-bit integer option information |
| DoubleOptionInfo | Wrapper class for accessing floating-point option information |
| FloatOptionInfo | Wrapper class for accessing floating-point option information |
| StringOptionInfo | Wrapper class for accessing string option information |
| EnumOptionInfo | Wrapper class for accessing enum option information |
| BooleanOptionStorage | Converts, validates, and stores boolean values |
| IntegerOptionStorage | Converts, validates, and stores integer values |
| Int64OptionStorage | Converts, validates, and stores integer values |
| DoubleOptionStorage | Converts, validates, and stores floating-point (double) values |
| FloatOptionStorage | Converts, validates, and stores floating-point (float) values |
| StringOptionStorage | Converts, validates, and stores string values |
| EnumOptionStorage | Converts, validates, and stores enum values |
| OptionsBehaviorCollection | Container for IOptionsBehavior objects |
| FileNameOption | Specifies an option that provides file names |
| FileNameOptionInfo | Wrapper class for accessing file name option information |
| FileNameOptionManager | Handles interaction of file name options with global options |
| Impl | Private implemention class for FileNameOptionManager |
| FileNameOptionStorage | Converts, validates, and stores file names |
| IOptionsBehavior | Interface to provide extension points for options parsing |
| IOptionsContainer | Interface for adding input options |
| IOptionsContainerWithSections | Interface for adding input options with sections |
| IOptionSectionStorage | Provides behavior specific to a certain option section type |
| IOptionValueStore | Represents the final storage location of option values |
| OptionManagerContainer | Container to keep managers added with Options::addManager() and pass them to options |
| IOptionManager | Base class for option managers |
| Options | Collection of options |
| OptionsAssigner | Decorator class for assigning values to Options |
| Impl | Private implementation class for OptionsAssigner |
| OptionSection | Declares a simple option section |
| OptionSectionHandle | Allows adding options to an OptionSection |
| OptionStorageTemplateSimple | Simplified option storage template for options that have one-to-one value conversion |
| OptionsVisitor | Pure interface for visiting options in a Options object |
| OptionsTypeVisitor | Abstract base class for visiting options of a particular type |
| OptionsIterator | Decorator class for visiting options in a Options object |
| OptionsModifyingVisitor | Pure interface for visiting options in a Options object, allowing modifications |
| OptionsModifyingTypeVisitor | Abstract base class for visiting options of a particular type, allowing modifications |
| OptionsModifyingIterator | Decorator class for visiting options in a Options object, allowing changes |
| RepeatingOptionSectionHandle | Allows adding options to an RepeatingOptionSection |
| RepeatingOptionSectionStorage | Implements handling of the structures that stores per-section values |
| RepeatingOptionSection | Declares an option section that creates a structure for each instance |
| TimeUnitManager | Provides common functionality for time unit conversions |
| TimeUnitBehavior | Options behavior to add a time unit option |
| OptionValueConverterSimple | Helper for converting from Variant to a given type |
| OptionValueStoreNull | Value storage that does not store anywhere |
| ExponentialDistribution | Exponential distribution |
| param_type | Exponential distribution parameters |
| GammaDistribution | Gamma distribution |
| param_type | Gamma distribution parameters |
| NormalDistribution | Normal distribution |
| param_type | Normal distribution parameters |
| TabulatedNormalDistribution | Tabulated normal random distribution |
| param_type | Normal distribution parameter class (mean and stddev) |
| ThreeFry2x64General | General implementation class for ThreeFry counter-based random engines |
| ThreeFry2x64 | ThreeFry2x64 random engine with 20 iteractions |
| ThreeFry2x64Fast | ThreeFry2x64 random engine with 13 iteractions |
| UniformIntDistribution | Uniform integer distribution |
| param_type | Uniform int distribution parameters |
| UniformRealDistribution | Uniform real distribution |
| param_type | Uniform real distribution parameters |
| SelectionCompiler | Implements selection compilation |
| AnalysisNeighborhoodPositions | Input positions for neighborhood searching |
| AnalysisNeighborhood | Neighborhood searching for analysis tools |
| AnalysisNeighborhoodPair | Value type to represent a pair of positions found in neighborhood searching |
| AnalysisNeighborhoodSearch | Initialized neighborhood search with a fixed set of reference positions |
| AnalysisNeighborhoodPairSearch | Initialized neighborhood pair search with a fixed set of positions |
| SelectionParserValue | Describes a parsed value, possibly resulting from expression evaluation |
| SelectionParserParameter | Describes a parsed method parameter |
| PositionCalculationCollection | Collection of gmx_ana_poscalc_t structures for the same topology |
| Impl | Private implementation class for PositionCalculationCollection |
| Selection | Provides access to a single selection |
| SelectionPosition | Provides access to information about a single selected position |
| SelectionEvaluator | Implements selection evaluation |
| SelectionCollection | Collection of selections |
| Impl | Private implemention class for SelectionCollection |
| SelectionTopologyProperties | Describes topology properties required for selection evaluation |
| SelectionFileOption | Specifies a special option that provides selections from a file |
| SelectionFileOptionInfo | Wrapper class for accessing and modifying selection file option information |
| SelectionFileOptionStorage | Implementation for a special option for reading selections from files |
| SelectionOption | Specifies an option that provides selection(s) |
| SelectionOptionInfo | Wrapper class for accessing and modifying selection option information |
| ITopologyProvider | Provides topology information to SelectionOptionBehavior |
| SelectionOptionBehavior | Options behavior to allow using SelectionOptions |
| SelectionOptionManager | Handles interaction of selection options with other options and user input |
| Impl | Private implemention class for SelectionOptionManager |
| RequestsClearer | Helper class that clears a request list on scope exit |
| SelectionRequest | Request for postponed parsing of selections |
| SelectionOptionStorage | Converts, validates, and stores selection values |
| SelectionLocation | Stores the location of a selection element in the selection text |
| SelectionTreeElement | Represents an element of a selection expression |
| SelMethodEvalContext | Evaluation context for selection methods |
| SelectionParserSymbol | Single symbol for the selection parser |
| Impl | Private implementation class for SelectionParserSymbol |
| SelectionParserSymbolIterator | Input iterator for iterating symbols of a given type |
| Impl | Private implementation class for SelectionParserSymbolIterator |
| SelectionParserSymbolTable | Symbol table for the selection parser |
| Impl | Private implementation class for SelectionParserSymbolTable |
| Simd4Double | SIMD4 double type |
| Simd4DBool | SIMD4 variable type to use for logical comparisons on doubles |
| Simd4Float | SIMD4 float type |
| Simd4FBool | SIMD4 variable type to use for logical comparisons on floats |
| SimdDouble | Double SIMD variable. Available if GMX_SIMD_HAVE_DOUBLE is 1 |
| SimdDInt32 | Integer SIMD variable type to use for conversions to/from double |
| SimdDBool | Boolean type for double SIMD data |
| SimdDIBool | Boolean type for integer datatypes corresponding to double SIMD |
| SimdFloat | Float SIMD variable. Available if GMX_SIMD_HAVE_FLOAT is 1 |
| SimdFInt32 | Integer SIMD variable type to use for conversions to/from float |
| SimdFBool | Boolean type for float SIMD data |
| SimdFIBool | Boolean type for integer datatypes corresponding to float SIMD |
| SimdFloatTag | Tag type to select to load SimdFloat with simdLoad(U) |
| SimdDoubleTag | Tag type to select to load SimdDouble with simdLoad(U) |
| SimdFInt32Tag | Tag type to select to load SimdFInt32 with simdLoad(U) |
| SimdDInt32Tag | Tag type to select to load SimdDInt32 with simdLoad(U) |
| AlignedArray< float, N > | Identical to std::array with GMX_SIMD_FLOAT_WIDTH alignment. Should not be deleted through base pointer (destructor is non-virtual) |
| AlignedArray< double, N > | Identical to std::array with GMX_SIMD_DOUBLE_WIDTH alignment. Should not be deleted through base pointer (destructor is non-virtual) |
| SimdSetZeroProxyInternal | Proxy object to enable setZero() for SIMD and real types |
| CubicSplineTable | Cubic spline interpolation table |
| QuadraticSplineTable | Quadratic spline interpolation table |
| AnalyticalSplineTableInput | Specification for analytical table function (name, function, derivative) |
| NumericalSplineTableInput | Specification for vector table function (name, function, derivative, spacing) |
| GpuTaskMapping | Specifies the GPU deviceID_ available for task_ to use |
| TrajectoryAnalysisModuleData | Base class for thread-local data storage during trajectory analysis |
| Impl | Private implementation class for TrajectoryAnalysisModuleData |
| TrajectoryAnalysisModule | Base class for trajectory analysis modules |
| Impl | Private implementation class for TrajectoryAnalysisModule |
| TrajectoryAnalysisSettings | Trajectory analysis module configuration object |
| Impl | Private implementation class for TrajectoryAnalysisSettings |
| TopologyInformation | Topology information passed to a trajectory analysis module |
| TrajectoryAnalysisCommandLineRunner | Runner for command-line trajectory analysis tools |
| SurfaceAreaCalculator | Computes surface areas for a group of atoms/spheres |
| UnionFinder | Union-find data structure for keeping track of disjoint sets |
| MappedUnionFinder | Extension of UnionFind that supports non-consecutive integer indices as items |
| TrajectoryAnalysisRunnerCommon | Implements common trajectory analysis runner functionality |
| AlignedAllocationPolicy | Policy class for configuring gmx::Allocator, to manage allocations of aligned memory for SIMD code |
| PageAlignedAllocationPolicy | Policy class for configuring gmx::Allocator, to manage allocations of page-aligned memory that can be locked for asynchronous transfer to GPU devices |
| Allocator | Policy-based memory allocator |
| rebind | Standard-required typedef to use allocator with different class |
| EmptyArrayRef | Tag type to initialize empty array references |
| BinaryInformationSettings | Settings for printBinaryInformation() |
| PrivateImplPointer | Helper class to manage a pointer to a private implementation class |
| DataFileOptions | Search parameters for DataFileFinder |
| DataFileInfo | Information about a data file found by DataFileFinder::enumerateFiles() |
| DataFileFinder | Searches data files from a set of paths |
| DirectoryEnumerator | Lists files in a directory |
| ExceptionInfo | Stores additional context information for exceptions |
| ThrowLocation | Stores the location from which an exception was thrown |
| ExceptionInitializer | Provides information for Gromacs exception constructors |
| GromacsException | Base class for all exception objects in Gromacs |
| FileIOError | Exception class for file I/O errors |
| UserInputError | Exception class for user input errors |
| InvalidInputError | Exception class for situations where user input cannot be parsed/understood |
| InconsistentInputError | Exception class for situations where user input is inconsistent |
| ToleranceError | Exception class when a specified tolerance cannot be achieved |
| SimulationInstabilityError | Exception class for simulation instabilities |
| InternalError | Exception class for internal errors |
| APIError | Exception class for incorrect use of an API |
| RangeError | Exception class for out-of-range values or indices |
| NotImplementedError | Exception class for use of an unimplemented feature |
| IFileInputRedirector | Allows overriding file existence checks from code that supports it |
| IFileOutputRedirector | Allows capturing stdout and file output from code that supports it |
| StandardInputStream | Text input stream implementation for reading from stdin |
| TextInputFile | Text input stream implementation for reading from a file |
| TextOutputFile | Text output stream implementation for writing to a file |
| FlagsTemplate | Template class for typesafe handling of combination of flags |
| Regex | Represents a regular expression |
| ISerializer | Interface for types that convert standard data types into a form suitable for storage or transfer |
| KeyValueTreePath | Identifies an entry in a key-value tree |
| KeyValueTreeBuilder | Root builder for creating trees that have an object at the root |
| KeyValueTreeValueBuilder | Builder for KeyValueTreeValue objects |
| KeyValueTreeUniformArrayBuilder | Builder for KeyValueTreeArray objects where all elements are of type T |
| KeyValueTreeObjectArrayBuilder | Builder for KeyValueTreeArray objects where all elements are KeyValueTreeObject objects |
| KeyValueTreeObjectBuilder | Builder for KeyValueTreeObject objects |
| IKeyValueTreeTransformRules | Interface to declare rules for transforming key-value trees |
| KeyValueTreeTransformRulesScoped | Helper object returned from IKeyValueTreeTransformRules::scopedTransform() |
| KeyValueTreeTransformRuleBuilder | Provides methods to specify one transformation rule |
| AfterFrom | Properties that can be specified after from() |
| Base | Base class used for implementing parameter provider objects |
| ToObject | Properties that can be specified after from().toObject() |
| ToValue | Properties that can be specified after from().to() |
| ILogTarget | Target where log output can be written |
| LogEntryWriter | Helper class for creating log entries with GMX_LOG |
| LogWriteHelper | Helper class for implementing GMX_LOG |
| LogLevelHelper | Represents a single logging level |
| MDLogger | Declares a logging interface |
| LoggerBuilder | Initializes loggers |
| LoggerOwner | Manages memory for a logger built with LoggerBuilder |
| MessageStringCollector | Helper class for collecting message strings, optionally with context |
| MessageStringContext | Convenience class for creating a message context |
| no_delete | Deleter for std::shared_ptr that does nothing |
| InstallationPrefixInfo | Provides information about installation prefix (see IProgramContext::installationPrefix()) |
| IProgramContext | Provides context information about the program that is calling the library |
| StringCompare | Compare object for std::string STL containers and algorithms that supports run-time decision on how to compare |
| StringOutputStream | Text output stream implementation for writing to an in-memory string |
| StringInputStream | Helper class to convert static string data to a stream |
| StringFormatter | Function object that wraps a call to formatString() that expects a single conversion argument, for use with algorithms |
| IdentityFormatter | Function object to implement the same interface as StringFormatter to use with strings that should not be formatted further |
| TextLineWrapperSettings | Stores settings for line wrapping |
| TextLineWrapper | Wraps lines to a predefined length |
| TextReader | Reads text from a TextInputStream |
| Impl | Implementation class |
| TextInputStream | Interface for reading text |
| TextOutputStream | Interface for writing text |
| TextWriter | Writes text into a TextOutputStream |
| isIntegralConstant | Is true if type is a std::integral_constant |
| functor_wrapper | Wrap function into functor to be used as deleter |
| Variant | Represents a dynamically typed value of an arbitrary type |
| Mdrunner | Runner object for supporting setup and execution of mdrun |
| AnalysisTemplate | Template class to serve as a basis for user analysis tools |
| AtomIndex | List of atom indices belonging to a task |
| AwhReader | All options and meta-data needed for the AWH output |
| BalanceRegion | Struct for timing the region for dynamic load balancing |
| BiasReader | All meta-data that is shared for all output files for one bias |
| bonded_threading_t | Struct contain all data for bonded force threading |
| CheckpointOptions | Options for writing checkpoint files |
| cl_atomdata | Nonbonded atom data - both inputs and outputs |
| cl_nb_staging | Staging area for temporary data downloaded from the GPU |
| cl_nbparam | Parameters required for the OpenCL nonbonded calculations |
| cl_nbparam_params | Data structure shared between the OpenCL device code and OpenCL host code |
| cl_plist | Pair list data |
| ContinuationOptions | Options and settings for continuing from checkpoint |
| cu_atomdata | Nonbonded atom data - both inputs and outputs |
| cu_nbparam | Parameters required for the CUDA nonbonded calculations |
| cu_plist | Pair list data |
| df_history_t | Free-energy sampling history struct |
| DomdecOptions | Structure containing all (command line) options for the domain decomposition |
| ekinstate_t | Struct used for checkpointing only |
| em_state_t | Utility structure for manipulating states during EM |
| EwaldBoxZScaler | Class to handle box scaling for Ewald and PME |
| f_thread_t | Struct with output for bonded forces, used per thread |
| ForceProviders | Evaluates forces from a collection of gmx::IForceProvider |
| gmx_ana_index_t | Stores a single index group |
| gmx_ana_indexgrps_t | Stores a set of index groups |
| gmx_ana_indexmap_t | Data structure for calculating index group mappings |
| gmx_ana_pos_t | Stores a set of positions together with their origins |
| gmx_ana_poscalc_t | Data structure for position calculation |
| gmx_ana_selcollection_t | Information for a collection of selections |
| gmx_ana_selmethod_help_t | Help information for a selection method |
| gmx_ana_selmethod_t | Describes a selection method |
| gmx_ana_selparam_t | Describes a single parameter for a selection method |
| gmx_ana_selvalue_t | Describes a value of a selection expression or of a selection method parameter |
| gmx_device_info_t | OpenCL device information |
| gmx_device_runtime_data_t | OpenCL GPU runtime data |
| gmx_domdec_constraints_t | Struct used during constraint setup with domain decomposition |
| gmx_domdec_specat_comm_t | Struct with setup and buffers for special atom communication |
| gmx_fft_fftpack | Contents of the FFTPACK fft datatype |
| gmx_fft_fftw3 | Contents of the FFTW3 fft datatype |
| gmx_fft_mkl | Contents of the Intel MKL FFT fft datatype |
| gmx_ga2la_t | Structure for all global to local mapping information |
| gmx_hash_e_t | Hashing key-generation helper struct |
| gmx_hash_t | Hashing helper struct |
| gmx_help_make_index_group | Cata necessary to construct a single (protein) index group in analyse_prot() |
| gmx_hw_opt_t | Threading and GPU options, can be set automatically or by the user |
| gmx_kernel_timing_data_t | GPU kernel time and call count |
| gmx_laa_t | Structure for the local atom info for a plain list |
| gmx_lal_t | Structure for the local atom info for a hash table |
| gmx_molblock_t | Block of molecules of the same type, used in gmx_mtop_t |
| gmx_nbnxn_cuda_t | Main data structure for CUDA nonbonded force calculations |
| gmx_nbnxn_ocl_t | Main data structure for OpenCL nonbonded force calculations |
| gmx_pme_comm_n_box_t | Helper struct for PP-PME communication of parameters |
| gmx_pme_comm_vir_ene_t | Helper struct for PP-PME communication of virial and energy |
| gmx_pme_pp | Master PP-PME communication data structure |
| gmx_reverse_top_t | Struct for the reverse topology: links bonded interactions to atomsx |
| gmx_sel_evaluate_t | Data structure for passing information required during evaluation |
| gmx_sel_lexer_t | Internal data structure for the selection tokenizer state |
| gmx_sel_mempool_block_t | Describes a single block allocated from the memory pool |
| gmx_sel_mempool_t | Describes a memory pool |
| gmx_sparsematrix | Sparse matrix storage format |
| gmx_tng_trajectory | Gromacs Wrapper around tng datatype |
| gmx_wallclock_gpu_nbnxn_t | GPU NB timings for kernels and H2d/D2H transfers |
| gmx_wallclock_gpu_pme_t | GPU timings for PME |
| gmx_walltime_accounting | Manages caching wall-clock time measurements for simulations |
| GpuRegionTimerImpl | This is a GPU region timing implementation interface. It should provide methods for measuring the last timespan. Copying/assignment is disabled since the underlying timing events are owned by this |
| GpuRegionTimerImpl< GpuFramework::OpenCL > | The OpenCL implementation of the GPU code region timing. With OpenCL, one has to use cl_event handle for each API call that has to be timed, and accumulate the timing afterwards. As we would like to avoid overhead on API calls, we only query and accumulate cl_event timing at the end of time steps, not after the API calls. Thus, this implementation does not reuse a single cl_event for multiple calls, but instead maintains an array of cl_events to be used within any single code region. The array size is fixed at a small but sufficiently large value for the number of cl_events that might contribute to a timer region, currently 10 |
| GpuRegionTimerWrapper | This is a GPU region timing wrapper class. It allows for host-side tracking of the accumulated execution timespans in GPU code (measuring kernel or transfers duration). It also partially tracks the correctness of the timer state transitions, as far as current implementation allows (see TODO in getLastRangeTime() for a disabled check). Internally it uses GpuRegionTimerImpl for measuring regions |
| GpuTraits | GPU build-path traits such as types |
| history_t | History information for NMR distance and orientation restraints |
| ilist_data_t | Struct for passing all data required for a function type |
| IMDEnergyBlock | IMD (interactive molecular dynamics) energy record |
| IMDHeader | IMD (interactive molecular dynamics) communication structure |
| ImdOptions | Options for IMD |
| IMDSocket | IMD (interactive molecular dynamics) socket structure |
| InterdependentTask | Data structure for thread tasks that use constructing atoms outside their own atom range |
| MdrunOptions | Collection of all options of mdrun that are not processed separately |
| nb_staging | Staging area for temporary data downloaded from the GPU |
| nbnxn_gpu_timers_t | GPU region timers used for timing GPU kernels and H2D/D2H transfers |
| nonbonded_verlet_group_t | Non-bonded interaction group data structure |
| nonbonded_verlet_t | Top-level non-bonded data structure for the Verlet-type cut-off scheme |
| ObservablesHistory | Observables history, for writing/reading to/from checkpoint file |
| ocl_gpu_id_t | OpenCL GPU device identificator |
| omp_module_nthreads_t | Structure with the number of threads for each OpenMP multi-threaded algorithmic module in mdrun |
| OutputFile | All meta-data that is shared for one output file type for one bias |
| pme_setup_t | Parameters and settings for one PP-PME setup |
| PmeGpu | The main PME GPU host structure, included in the PME CPU structure by pointer |
| PmeGpuAtomParams | A GPU data structure for storing the PME data of the atoms, local to this process' domain partition. This only has to be updated every DD step |
| PmeGpuConstParams | A GPU data structure for storing the constant PME data. This only has to be initialized once |
| PmeGpuDynamicParams | A GPU data structure for storing the PME data which might change for each new PME computation |
| PmeGpuGridParams | A GPU data structure for storing the PME data related to the grid sizes and cut-off. This only has to be updated at every DD step |
| PmeGpuKernelParamsBase | A single structure encompassing almost all the PME data used in GPU kernels on device. This is inherited by the GPU framework-specific structure (PmeGpuCudaKernelParams in pme.cuh). This way, most code preparing the kernel parameters can be GPU-agnostic by casting the kernel parameter data pointer to PmeGpuKernelParamsBase |
| PmeGpuSettings | The PME GPU settings structure, included in the main PME GPU structure by value |
| PmeGpuStaging | The PME GPU intermediate buffers structure, included in the main PME GPU structure by value. Buffers are managed by the PME GPU module |
| PmeShared | The PME GPU structure for all the data copied directly from the CPU PME structure. The copying is done when the CPU PME structure is already (re-)initialized (pme_gpu_reinit is called at the end of gmx_pme_init). All the variables here are named almost the same way as in gmx_pme_t. The types are different: pointers are replaced by vectors. TODO: use the shared data with the PME CPU. Included in the main PME GPU structure by value |
| PpRanks | Contains information about the PP ranks that partner this PME rank |
| swap_compartment | Structure containing compartment-specific data |
| swap_group | This structure contains data needed for the groups involved in swapping: split group 0, split group 1, solvent group, ion groups |
| t_bb | Struct containing properties of a residue in a protein backbone |
| t_compare_value | Data structure for comparison expression operand values |
| t_compiler_data | Internal data structure used by the compiler |
| t_coordselection | Selection of pull coordinates to be used in WHAM (one structure for each tpr file) |
| t_filenm | File name option definition for C code |
| t_gmx_IMD | IMD (interactive molecular dynamics) main data structure |
| t_mdatoms | Declares mdatom data structure |
| t_methoddata_compare | Data structure for comparison expression evaluation |
| t_methoddata_distance | Data structure for distance-based selection method |
| t_methoddata_insolidangle | Data structure for the insolidangle selection method |
| t_methoddata_kweval | Data structure for keyword evaluation in arbitrary groups |
| t_methoddata_kwint | Data structure for integer keyword expression evaluation |
| t_methoddata_kwreal | Data structure for real keyword expression evaluation |
| t_methoddata_merge | Data structure for the merging selection modifiers |
| t_methoddata_permute | Data structure for the permute selection modifier |
| t_methoddata_pos | Data structure for position keyword evaluation |
| t_methoddata_same | Data structure for the same selection method |
| t_pargs | Command-line argument definition for C code |
| t_partition | Internal data structure for the insolidangle selection method |
| t_partition_item | Internal data structure for the insolidangle selection method |
| t_pbc | Structure containing info on periodic boundary conditions |
| t_pullcoord | Parameters of one pull coodinate |
| t_register_method | Helper structure for defining selection methods |
| t_spheresurfacebin | Internal data structure for the insolidangle selection method |
| t_state | The microstate of the system |
| t_swap | Main (private) data structure for the position swapping protocol |
| t_UmbrellaHeader | Parameters of the umbrella potentials |
| t_UmbrellaOptions | Parameters of WHAM |
| t_UmbrellaWindow | Data in the umbrella histograms |
| thread_work_t | Struct for thread local work data for local topology generation |
| TimingOptions | Options for timing (parts of) mdrun |
| VsiteThread | Vsite thread task data structure |
1.8.5
